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- PDB-9rtr: Crystal structure of BRAF:MEK1 complex with asymmetric dimer inte... -

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Basic information

Entry
Database: PDB / ID: 9rtr
TitleCrystal structure of BRAF:MEK1 complex with asymmetric dimer interface bound to AMPPNP
Components
  • Dual specificity mitogen-activated protein kinase kinase 1
  • Serine/threonine-protein kinase B-raf
KeywordsSIGNALING PROTEIN / Kinase / Complex
Function / homology
Function and homology information


negative regulation of homotypic cell-cell adhesion / regulation of vascular associated smooth muscle contraction / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / mitogen-activated protein kinase kinase / melanosome transport / Golgi inheritance / MAP kinase scaffold activity / Signalling to p38 via RIT and RIN / positive regulation of muscle contraction / ARMS-mediated activation ...negative regulation of homotypic cell-cell adhesion / regulation of vascular associated smooth muscle contraction / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / mitogen-activated protein kinase kinase / melanosome transport / Golgi inheritance / MAP kinase scaffold activity / Signalling to p38 via RIT and RIN / positive regulation of muscle contraction / ARMS-mediated activation / Signaling by MAP2K mutants / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of D-glucose transmembrane transport / establishment of protein localization to membrane / vesicle transport along microtubule / regulation of Golgi inheritance / mitogen-activated protein kinase kinase kinase binding / triglyceride homeostasis / positive regulation of protein serine/threonine kinase activity / regulation of early endosome to late endosome transport / Negative feedback regulation of MAPK pathway / regulation of stress-activated MAPK cascade / Frs2-mediated activation / MAPK3 (ERK1) activation / ERBB2-ERBB3 signaling pathway / MAP kinase kinase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of ATP biosynthetic process / neuromuscular junction development / ERK1 and ERK2 cascade / response to axon injury / Uptake and function of anthrax toxins / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / protein kinase activator activity / Schwann cell development / postsynaptic modulation of chemical synaptic transmission / myelination / insulin-like growth factor receptor signaling pathway / animal organ morphogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to calcium ion / neuron projection morphogenesis / response to glucocorticoid / positive regulation of autophagy / protein serine/threonine kinase activator activity / dendrite cytoplasm / Signal transduction by L1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / positive regulation of transcription elongation by RNA polymerase II / RAF activation / Signaling by high-kinase activity BRAF mutants / Spry regulation of FGF signaling / MAP2K and MAPK activation / cellular senescence / epidermal growth factor receptor signaling pathway / chemotaxis / small GTPase binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MAPK cascade / Negative regulation of MAPK pathway / Signaling by BRAF and RAF1 fusions / late endosome / neuron differentiation / protein tyrosine kinase activity / ciliary basal body / response to oxidative stress / cell body / scaffold protein binding / cell cortex / microtubule / early endosome / perikaryon / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / protein phosphorylation / non-specific serine/threonine protein kinase / postsynapse / postsynaptic density / neuron projection / positive regulation of cell migration / negative regulation of cell population proliferation / negative regulation of gene expression / protein serine kinase activity / axon / focal adhesion / protein serine/threonine kinase activity / centrosome / positive regulation of gene expression / calcium ion binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / glutamatergic synapse / Golgi apparatus
Similarity search - Function
: / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / : / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. ...: / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / : / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase B-raf / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKondo, Y. / Notbohm, J. / Camacho, I.N. / Nagy-Davidescu, G. / Mason, T. / Muhle, J. / Standfuss, J. / Perica, T.
Funding support Switzerland, European Union, 6items
OrganizationGrant numberCountry
Swiss Cancer LeagueKFS-5737-02-2023 Switzerland
Innosuisse42711.1 IP-LSEuropean Union
Swiss National Science FoundationCRSII5_213507 Switzerland
Swiss National Science Foundation310030_207462 Switzerland
Swiss National Science Foundation320030_227566 Switzerland
UZH Candoc GrantFK-23-043 Switzerland
CitationJournal: To Be Published
Title: Structural insights into phosphorylation of the MEK1 activation loop by a BRAF asymmetric dimer
Authors: Kondo, Y. / Notbohm, J. / Camacho, I.N. / Nagy-Daivescu, G. / Mason, T. / Muhle, J. / Standfuss, J. / Perica, T.
History
DepositionJul 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Dual specificity mitogen-activated protein kinase kinase 1
C: Serine/threonine-protein kinase B-raf
A: Dual specificity mitogen-activated protein kinase kinase 1
B: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,50911
Polymers143,8934
Non-polymers1,6167
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.716, 67.906, 292.536
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1(chain "D" and (resid 42 through 276 or resid 307 through 901 or resid 902))
d_1ens_2(chain "B" and (resid 447 through 601 or resid 612 through 721))
d_2ens_2(chain "C" and (resid 447 through 601 or resid 612 through 721))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LEULEULEULEUAC42 - 3817 - 346
d_12ens_1ANPANPANPANPAG901
d_21ens_1LEULEUGLYGLYDA42 - 2767 - 241
d_22ens_1PROPROLEULEUDA307 - 381272 - 346
d_23ens_1ANPANPANPANPDE901
d_11ens_2SERSERLYSLYSBD447 - 6016 - 160
d_12ens_2GLNGLNLEULEUBD612 - 721171 - 280
d_21ens_2SERSERLYSLYSCB447 - 6016 - 160
d_22ens_2GLNGLNLEULEUCB612 - 721171 - 280

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.926074889766, 0.374693696047, -0.0446086615674), (0.36549658592, 0.920104517967, 0.140783243669), (0.0937952249603, 0.114071513356, -0.989034956721)78.9450184329, -16.8258417716, 32.1509557593
2given(-0.930913314266, 0.365207730395, 0.00486980303316), (0.36236157818, 0.921823600364, 0.137605728338), (0.0457655763706, 0.129863634142, -0.990475112533)76.0379714987, -16.0828733857, 33.8501122662

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Components

#1: Protein Dual specificity mitogen-activated protein kinase kinase 1 / MAP kinase kinase 1 / MAPKK 1 / MKK1 / ERK activator kinase 1 / MAPK/ERK kinase 1 / MEK 1


Mass: 39831.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q02750, mitogen-activated protein kinase kinase
#2: Protein Serine/threonine-protein kinase B-raf / Proto-oncogene B-Raf / p94 / v-Raf murine sarcoma viral oncogene homolog B1


Mass: 32114.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: BRAF V600E mutant kinase domain with 14 mutations to improve soluble protein expression
Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF, BRAF1, RAFB1 / Production host: Escherichia coli (E. coli)
References: UniProt: P15056, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8% PEG20K/PEG550MME, 0.1 M Tris pH8.6, 200 mM potassium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.6→146.27 Å / Num. obs: 23614 / % possible obs: 56.3 % / Redundancy: 13.4 % / Biso Wilson estimate: 46.14 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.26 / Net I/σ(I): 8.1
Reflection shellResolution: 2.6→2.93 Å / Rmerge(I) obs: 1.663 / Num. unique obs: 123 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
AutoProcessdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→60.7 Å / SU ML: 0.2817 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.7372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.262 1178 4.99 %
Rwork0.208 22432 -
obs0.2111 23610 56.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.66 Å2
Refinement stepCycle: LAST / Resolution: 2.6→60.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9194 0 97 59 9350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00229478
X-RAY DIFFRACTIONf_angle_d0.54112784
X-RAY DIFFRACTIONf_chiral_restr0.04291400
X-RAY DIFFRACTIONf_plane_restr0.00411627
X-RAY DIFFRACTIONf_dihedral_angle_d13.58243605
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS0.839900935591
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS1.67115321221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.365930.3451185X-RAY DIFFRACTION3.64
2.72-2.860.3586280.3228575X-RAY DIFFRACTION11.8
2.86-3.040.305350.3061037X-RAY DIFFRACTION20.74
3.04-3.280.3347870.28571833X-RAY DIFFRACTION37.09
3.28-3.610.3131920.23553558X-RAY DIFFRACTION72.16
3.61-4.130.26462640.19544975X-RAY DIFFRACTION99.83
4.13-5.20.25193040.18155007X-RAY DIFFRACTION100
5.2-60.70.23222650.20625262X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.110450832056-0.160588083022-0.2081919693110.9697664382371.144456552241.35148735861-0.398621102755-0.2902434209690.479703535249-0.01740899447580.2268169489670.0298040827079-1.47773583443-0.6377944948080.02457667435521.253218759470.455781354305-0.007496169645960.730372538792-0.1528310553650.74236647304226.4421052714.8199408347-21.7065260856
24.19433148433-0.1016906189220.6480576511163.371558338580.5880390372891.49411552551-0.0844808018360.01175719107720.802331548711-0.03378933983240.02804042315030.176808598976-1.01237276204-0.4517107296930.02993535840180.8237484189180.368845691464-0.03104906621750.5054080173550.04039701749920.52335351777628.9635882846.01764490716-30.2909060265
37.95711861671-2.49570131712-0.1562721553074.65030236045.142650462877.513386057380.0656406596304-0.0685045416530.5732679041120.7445583938960.1688912859210.0691936585536-1.13928616421-0.311534853651-0.4366454593720.5519246348170.1532960231620.109758429030.3543578185130.005357258636080.4558508870243.0688174697-3.81154624708-27.6128693434
44.62808375930.15376507164-0.0003781382839692.58935523011-0.7163142589761.21496252810.02922504375410.522224768786-0.152686915902-0.484537593925-0.01057826987570.395319005568-0.186042307001-0.490806135516-0.03552484640560.4280955135240.150936023922-0.04894471981720.526203584676-0.1064782065490.32459060036930.7727696205-11.5521831635-38.4181068391
53.991436867641.27996554677-0.5230142491496.472891789180.2593417448663.99487142369-0.03712993262941.094657297310.768725814963-0.830637652436-0.219081766281-0.16348110764-0.473486548615-0.2577366298090.09023690263280.3240254786130.03580378352110.05710608073620.380992659410.09165389382430.23226589706730.80745485340.7069284507179.28015190435
64.44613345045-2.97664035891-1.479786603245.44388858878-1.421513053345.500106599910.67502169321.0990219862-0.449993281006-0.869005393664-0.2598718043471.27558415728-1.10789165346-1.68709602685-0.4590616031730.5911456768450.2726311270560.04691382186210.835035736472-0.1171939472590.51172077698430.2755645563-9.980905884371.49653414375
73.266619669050.263045788505-0.8124905776641.64842180877-0.1580048409313.012431483720.1192017452390.01281626997780.272048921515-0.1766426520360.2132569558270.0453509284629-0.5911975436460.302864117283-0.1725461956790.215108184879-0.1389769514490.04689817639770.393196074728-0.1804287315590.23440513368546.172473081-2.169534312082.36723378237
82.77989931659-0.01373153611310.7265458234873.605781482820.7111396353452.089404178170.06093931379750.1477183143580.172455533417-0.3346710440910.1298504787050.068354123832-0.3677578105980.61408444618-0.1088843849590.126554475077-0.05097452257750.1883637249960.336816797825-0.09626236302620.2619425144751.4296766704-7.4380300894-13.4546547284
91.37193140380.4020441317551.03693478230.807901982993-0.3381710164761.380573969290.213843241913-0.3963579186060.2406261510620.03807962390260.0297226719882-0.365764238401-0.3192833738420.953124215941-0.1674629560950.254196597405-0.1101841403480.1097828249240.822097984439-0.2468113792510.49048091361563.2744379611-6.22295266601-6.07684664466
102.61319967788-2.140510492560.1466264948852.49451596889-1.37766387633.40031611077-0.1583010342860.2096160711640.493481345894-0.346318146913-0.0304369324171-0.905719425842-0.4911800084050.6994146789480.2462279464980.594822547999-0.2721043234640.1087955300960.449878609898-0.03665150294020.7185371463655.12545087793.1934631205559.6938623779
112.521341242850.4826453010310.07574197228742.08508159877-0.01965323458150.975776614878-0.02911785537910.232779368730.238901787796-0.02981841046250.107473368735-0.463757973198-0.3261286599420.240021653913-0.08570279907840.432519239851-0.0614343905870.003103756881590.0710748442601-0.02354354396250.39511916145945.6099902623-5.4581631297466.3236432909
120.995403179067-0.1319826406420.4316258051332.825762710140.08009595034210.900153693483-0.03581141206030.119618750679-0.104545711381-0.1610367596990.0380255726487-0.5091256495660.3072126435150.209284008562-0.1233983599070.5839903141070.00302632010609-0.0181173479358-0.0549997106279-0.01487857046240.25868850712340.0133174203-20.528244410772.5206612333
133.44501558272-0.42143176395-0.5523159885792.19012957537-0.3894990009753.893165684240.0886602336586-0.03632452663140.02611674884620.1073586009120.189870656282-0.313486905385-0.2448998897040.699463399336-0.2613189676660.223652996124-0.0796260495896-0.03563522079550.346473728258-0.05145687360510.15208147373841.8330145462-4.4162632572129.7298845727
145.19112826209-0.8497086128330.7919824071112.575637460510.7509805713883.98242458728-0.2225344467880.6573531332860.6293644732540.01852684189810.22544383957-0.0708227394454-0.904703087552-0.255415723765-0.09165229645710.334776332920.007904122503990.08290338556890.2209439259180.03539880278790.17473154900426.4353066468-0.16940730105731.4842773829
154.45950280343-1.4870079818-2.301358975490.7089343299611.153418858772.25543831306-0.0789759607519-0.102003951103-0.5984673224780.1703390022840.174524263248-0.07061067080590.6136755500350.151309188675-0.05762541583040.361186853033-0.05068517859090.01082361096940.224750528780.002442870843310.22356926997427.919407185-14.446181075242.3395665217
160.6698465244680.2128104062940.5100364291091.921769255360.02963972247092.684964838240.0820558439030.1456324539320.2386863800790.291368861876-0.01943298759220.308650381252-0.355943679664-0.911726229751-0.03489651003880.1622667129090.1384844692940.0294613037940.3558924166370.04087838210230.20821922255119.0950869856-2.5095984488946.9488773306
178.485340706295.20713672891-3.726547626867.240017746250.2398982506633.523218967880.0754661553419-0.1229615786451.05726438044-0.7756214363480.5301227938891.55302787366-0.326300685806-1.73536645853-0.2750746520180.4516558979940.173643084746-0.1250428443981.079840600940.07288724031360.3972182960312.23800097591.8754596733430.4579808305
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 41 through 114 )DA41 - 1141 - 74
22chain 'D' and (resid 115 through 218 )DA115 - 21875 - 178
33chain 'D' and (resid 219 through 242 )DA219 - 242179 - 202
44chain 'D' and (resid 243 through 381 )DA243 - 381203 - 315
55chain 'C' and (resid 446 through 484 )CD446 - 4841 - 39
66chain 'C' and (resid 485 through 507 )CD485 - 50740 - 62
77chain 'C' and (resid 508 through 621 )CD508 - 62163 - 168
88chain 'C' and (resid 622 through 670 )CD622 - 670169 - 217
99chain 'C' and (resid 671 through 721 )CD671 - 721218 - 268
1010chain 'A' and (resid 42 through 114 )AE42 - 1141 - 73
1111chain 'A' and (resid 115 through 242 )AE115 - 24274 - 201
1212chain 'A' and (resid 243 through 381 )AE243 - 381202 - 310
1313chain 'B' and (resid 447 through 549 )BH447 - 5491 - 103
1414chain 'B' and (resid 550 through 592 )BH550 - 592104 - 146
1515chain 'B' and (resid 593 through 634 )BH593 - 634147 - 179
1616chain 'B' and (resid 635 through 706 )BH635 - 706180 - 251
1717chain 'B' and (resid 707 through 721 )BH707 - 721252 - 266

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